# Additive partitioning of TD, FD and PD (de Bello et al. 2010)
spe.rao <- Rao(
sample = t(spe),
dfunc = trait.d, # optional functional dissimilarity matrix
dphyl = phylo.d, # optional phylogenetic distance matrix
weight = FALSE,
Jost = TRUE,
structure = NULL
)
names(spe.rao)
# Species diversity (Simpson)
names(spe.rao$TD)
# Mean alpha Simpson diversity
spe.rao$TD$Mean_Alpha
# Gamma Simpson diversity
spe.rao$TD$Gamma
# Additive beta Simpson diversity
spe.rao$TD$Beta_add
spe.rao$TD$Gamma - spe.rao$TD$Mean_Alpha
# Beta diversity expressed as percentage of gamma
spe.rao$TD$Beta_prop
spe.rao$TD$Beta_add / spe.rao$TD$Gamma
# Multiplicative beta Simpson diversity
spe.rao$TD$Gamma / spe.rao$TD$Mean_Alpha
Cottus gobio
Salmo trutta
Phoxinus phoxinus
Barbatula barbatula
Thymallus thymallus
Telestes souffia
Chondrostoma nasus
Parachondrostoma toxostoma
Leuciscus leuciscus
Squalius cephalus
Barbus barbus
Alburnoides bipunctatus
Gobio gobio
Esox lucius
Perca fluviatilis
Rhodeus amarus
Lepomis gibbosus
Scardinius erythrophthalmus
Cyprinus carpio
Tinca tinca
Abramis brama
Ameiurus melas
Gymnocephalus cernua
Rutilus rutilus
Blicca bjoerkna
Alburnus alburnus
Anguilla anguilla
a
Chna
Pato
Rham
Abbr
Scer
Ruru
Alal
Cogo
Gogo
Gyce
Thth
Baba
Cyca
Lele
Titi
Blbj
Teso
Phph
Babl
Albi
Eslu
Anan
Satr
Legi
Sqce
Pefl
Icme
0.0
0.2
0.4
0.6
0.8
1.0
trait.d
hclust (*, "ward.D2")
Height
b
Fig. 8.11 Simplified phylogenetic tree of the fish species (a) and Ward hierarchical clustering of
the species based on their functional traits (b)
410
8 Community Diversity